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At least 19 records

Identifying impacts of contact tracing on HIV epidemiological inference from phylogenetic data

Abstract Robust sampling methods are foundational to inferences using phylogenies. Yet the impact of using contact tracing, a type of non-uniform sampling used in public health applications such as infectious disease outbreak investigations, has not been investigated in the molecular epidemiology field. To understand how contact tracing influences a recovered phylogeny, we developed a new simulation tool called SEEPS (Sequence Evolution and Epidemiological Process Simulator) that allows for the simulation of contact tracing and the resulting transmission tree, pathogen phylogeny, and corresponding virus genetic sequences. Importantly, SEEPS takes within-host evolution into account when generating pathogen phylogenies and sequences from transmission histories. Using SEEPS, we demonstrate that contact tracing can significantly impact the structure of the resulting tree, as described by popular tree statistics. Contact tracing generates phylogenies that are less balanced than the underlying transmission process, less representative of the larger epidemiological process, and affects the internal/external branch length ratios that characterize specific epidemiological scenarios. We also examined real data from a 2007–2008 Swedish HIV-1 outbreak and the broader 1998–2010 European HIV-1 epidemic to highlight the differences in contact tracing and expected phylogenies. Aided by SEEPS, we show that the data collection of the Swedish outbreak was strongly influenced by contact tracing even after downsampling, while the broader European Union epidemic showed little evidence of universal contact tracing, agreeing with the known epidemiological information about sampling and spread. Overall, our results highlight the importance of including possible non-uniform sampling schemes when examining phylogenetic trees. For that, SEEPS serves as a useful tool to evaluate such impacts, thereby facilitating better phylogenetic inferences of the characteristics of a disease outbreak. SEEPS is available at https://github.com/MolEvolEpid/SEEPS.

Virology

TRACE Input Modernization

This work presents a Tom’s Obvious Minimal Language (TOML)-based representation of input for the US Nuclear Regulatory Commission’s TRAC/RELAP Advanced Computational Engine (TRACE) thermal hydraulics code. Implemented using the Workbench Analysis Sequence Processor (WASP), the approach maps traditional TRACE input structures to a hierarchical format composed of named parameters, typed values, and native data collections. The resulting representation preserves TRACE’s existing modeling capabilities while providing a modern, structured interface for model development and management. WASP further extends TOML through a file import directive that supports modular model composition and reusable input organization. In addition, WASP provides extended array data entry convenience with various data repeat and interpolation capabilities. Examples of the new TOML syntax are provided for major TRACE input categories, including hydraulic components, heat structures, control systems, and trip logic. The TOML representation establishes a foundation for improved validation, tooling, automation, and model maintainability while remaining compatible with existing TRACE workflows. To facilitate migration to the TOML-based input format, the TRACE executable now supports conversion of native TRACE input into an intermediate JSON representation. A Python utility subsequently transforms the JSON data into an equivalent TOML model. Lastly, the TRACE executable now supports execution using TOML-formatted input.

Lefebvre, Robert A. [Oak Ridge National Laboratory

Modeling cross-beam energy transfer with sector ray tracing

Ray-based cross-beam energy transfer (CBET) models are an essential feature of the radiation-hydrodynamic codes used to simulate inertial confinement fusion implosions, but full 3D ray-based CBET calculations can have a prohibitively high computational cost. Sector ray tracing can be used to reduce the cost by orders of magnitude in cases where the coronal plasma and laser drive can be approximated as spherically symmetric. An extension of sector ray tracing (section ray tracing) can be used to relax the assumption of a spherically symmetric drive while still retaining most of the computational savings of a sector ray trace. We discuss the foundations of sector and section ray tracing and compare them to full ray tracing.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

A three-dimensional laser ray-tracing methodology for radiation-hydrodynamics simulations

We report on a methodology for performing laser ray-tracing in three spatial dimensions for radiation-hydrodynamics simulation codes. Our method, which is an extension of that developed in Haines et al., Comput. Fluids 201, 104478 (2020), utilizes an automatically generated separate mesh for the laser ray-tracing from the radiation-hydrodynamics mesh. This enables the laser mesh to be tailored to minimize ray noise with significantly fewer rays than would be required when the ray-tracing is performed on the radiation-hydrodynamics mesh, primarily by allowing the use of high-aspect-ratio cells that are not suitable for hydrodynamics solvers. For a planar target, we show that our method provides a ≈ 100× reduction in computational expense to achieve a fixed level of ray noise relative to ray-tracing directly on the radiation-hydrodynamics mesh. The relatively low ray requirement also enables efficient computation of cross-beam energy transfer. Each cell in the logically cubic laser mesh is a non-convex dodecahedron with triangular sides, and numerical integration of the ray trajectories and inverse bremsstrahlung is performed by mapping each cell to the unit cube. We will describe our methodology in detail as well as its implementation in the xRAGE radiation-hydrodynamics code, discuss performance, and present the results from applying the methodology to test problems with analytic solutions for laser ray-tracing through a quadratic density gradient with an analytic solution as well as for a laser-driven heat front. In 3D radiation-hydrodynamics simulations of laser-driven experiments performed on the National Ignition Facility, laser ray-tracing with our methodology uses less than 1% of total computational time while introducing acceptably low levels of ray noise.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

Results from a synthetic model of the ITER XRCS-Core diagnostic based on high-fidelity x-ray ray tracing

A high-fidelity synthetic diagnostic has been developed for the ITER core x-ray crystal spectrometer diagnostic based on x-ray ray tracing. This synthetic diagnostic has been used to model expected performance of the diagnostic, to aid in diagnostic design, and to develop engineering tolerances. The synthetic model is based on x-ray ray tracing using the recently developed xicsrt ray tracing code and includes a fully three-dimensional representation of the diagnostic based on the computer aided design. The modeled components are: plasma geometry and emission profiles, highly oriented pyrolytic graphite pre-reflectors, spherically bent crystals, and pixelated x-ray detectors. Plasma emission profiles have been calculated for Xe 44+ , Xe 47+ , and Xe 51+ , based on an ITER operational scenario available through the Integrated Modelling & Analysis Suite database, and modeled within the ray tracing code as a volumetric x-ray source; the shape of the plasma source is determined by equilibrium geometry and an appropriate wavelength distribution to match the expected ion temperature profile. All individual components of the x-ray optical system have been modeled with high-fidelity producing a synthetic detector image that is expected to closely match what will be seen in the final as-built system. Particular care is taken to maintain preservation of photon statistics throughout the ray tracing allowing for quantitative estimates of diagnostic performance.

47 OTHER INSTRUMENTATION

Selective Electrochemical Reduction of CO 2 to Metal Oxalates in Nonaqueous Solutions Using Trace Metal Pb on Carbon Supports Enhanced by a Tailored Microenvironment

In this work, the electroreduction of carbon dioxide (CO 2 ) to oxalate is enabled by incorporating trace metallic lead (Pb) on carbon‐based supports (CBS) with polymer overlayers. These composite materials serve as an efficient electrocatalytic system for the facile conversion and storage of CO 2 , a pernicious atmospheric pollutant. Results from controlled potential electrolysis experiments indicate that 1) trace metallic Pb on the ppb scale is active toward the reductive coupling of CO 2 to oxalate at comparable Faradaic efficiencies to bulk metallic Pb and 2) polymer encapsulation of this trace metallic Pb leads to promotion of CO 2 reduction (CO 2 R) selectively to metal oxalates over other products such as CO. Importantly, metal oxalates are important alternative cementitious materials and precursors for other materials’ synthesis applications. The solid products undergo rigorous spectroscopic characterization, including 13 CO 2 labeling experiments, to ensure the metal oxalates are in fact produced from CO 2 R. These findings serve as a model for leveraging microenvironment effects to enhance activity and selectivity for CO 2 R using trace‐metal catalysts for carbon utilization and storage technologies.

alternative cementitious materials

Quasi-optical beam tracing module development for millimeter-wave high-wavenumber collective scattering on the NSTX-U and EAST tokamaks

A Python3-based beam tracing code utilizing Quasi-Optics has been developed to track both incident and receiving beams in high-k collective millimeter wave scattering systems within magnetic fusion plasmas. In contrast to existing ray tracing codes that solely consider refraction, this beam tracing code incorporates diffraction phenomena, providing a more comprehensive calculation. Here, this enhanced capability allows for a more accurate calculation of the scattering volume and spatial resolution in high-k collective scattering systems, crucial for evaluating system performance and facilitating data analysis. Unlike Geometrical Optics, Quasi-Optics employs the complex eikonal method, representing a Gaussian beam as a collection of coupled rays to accurately preserve diffraction characteristics. The developed code is intended for application in NSTX-Upgrade and EAST high-k beam tracing analyses, targeting frequencies of 693 GHz and 270 GHz, respectively. The high-k system's primary objective is the observation of electron-scale instabilities. Employing a symplectic integrator, the code ensures numerical accuracy, assessed through the conservation of the Hamiltonian. With its precision and efficiency, the code facilitates rapid inter-shot analyses.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

Dirac traces and the Tutte polynomial

Perturbative calculations involving fermion loops in quantum field theories require tracing over Dirac matrices. A simple way to regulate the divergences that generically appear in these calculations is dimensional regularisation, which has the consequence of replacing 4-dimensional Dirac matrices with d-dimensional counterparts for arbitrary complex values of d. In this work, a connection between traces of d-dimensional Dirac matrices and computations of the Tutte polynomial of associated graphs is proven. The time complexity of computing Dirac traces is analysed by this connection, and improvements to algorithms for computing Dirac traces are proposed.

Renormalization and Regularization

Trace elements and their isotopes in streams and rivers

The occurrence and speciation of trace elements in streams and rivers are controlled by interconnected hydrogeological, biogeochemical, and anthropogenic factors that include rock weathering, climate, vegetation, and land use within the watershed. This chapter provides a broad overview of trace element abundance, speciation, and mobility in streams and rivers, including an assessment of how trace elements are partitioned into dissolved, colloidal, and particulate phases. We also discuss how trace elements are mobilized into stream networks and transformed during transport. Select isotopic systems are reviewed to provide examples of how isotopic analyses can be used to understand geochemical and anthropogenic processes.

Herndon, Elizabeth [ORNL] (ORCID:0000000291945493)

Quantification of trace iodine using laser-induced breakdown spectroscopy for real-time monitoring of nuclear off-gas streams

This study evaluated the potential of laser-induced breakdown spectroscopy (LIBS) for real-time monitoring of trace gas-phase iodine, which is an element of high significance in nuclear applications due to its long radioactive half-life (as iodine-129), volatility, and biological impact. In anticipation of iodine evolving into off-gas systems in molten salt reactor and nuclear fuel recycling applications, this research aimed to assess LIBS performance in flowing argon and helium matrices; optimize measurement parameters using a multichannel spectrometer; and perform calibrations to assess predictive capabilities and limits of detection (LODs). Experimental results successfully measured gas-phase iodine in flowing argon and helium; however, trace iodine was not detected in air. Optimal delay times were determined to be 10 µs for argon and 1 µs for helium, which are consistent with the expected shorter plasma lifetime in helium relative to argon. An emission line survey was provided with the 206.16, 804.37, 902.24, and 905.83 nm peaks, which were identified as the strongest emission peaks. Calibration models were successfully built in both helium and argon, achieving LODs down to 3 ppm in helium and 5 ppm in argon. The iodine emission at 905.83 nm emerged as the most robust for calibration and was subsequently applied to a time series dataset in argon. The predictive trace confirmed the feasibility of employing LIBS for continuous, online quantification of trace iodine in flowing gas systems.

Andrews, Hunter B. [Oak Ridge National Laboratory

An Integrated Framework for Memory-Centric Analysis: From Trace Collection to Co-Design

The memory wall phenomenon—where advances in processor performance significantly outpace those in memory subsystems—poses a fundamental challenge for contemporary computing systems. In memory-bound applications, memory subsystem behavior dominates performance, yet existing analysis approaches present significant limitations: detailed microarchitectural simulators require days to weeks to simulate modest workloads; hardware performance counters provide only aggregate statistics that obscure temporal and spatial access patterns; and scaled simulation approaches face challenges in capturing certain behaviors that emerge at larger scales. These limitations reflect a processor-centric design philosophy increasingly misaligned with memory-bound workloads where detailed understanding of memory access patterns, cache hierarchy interactions, and contention is critical for effective optimization. This paper presents an integrated framework for memory-centric analysis that enables effective hardware-software co-design. We describe practical trace collection techniques, including hardware-assisted processor tracing with minimal overhead and portable software-based instrumentation with statistical sampling. We present multi-perspective analysis methods that examine memory behavior from temporal, sequential, spatial, and relational viewpoints, revealing distinct optimization opportunities invisible in aggregate metrics. We detail an architectural modeling framework that uses sampled traces with temporal interpolation and confidence-based filtering to evaluate cache and memory configurations. Evaluation on representative benchmarks demonstrates that this framework achieves practical accuracy (L2 cache errors of 2.64\%, confidence-filtered L3 errors of 9.92\%, bandwidth errors of 7.33\%) while providing substantial speedup (26.8×) over cycle-accurate simulation, enabling rapid design space exploration. We demonstrate how this integrated framework enables systematic identification of both hardware optimizations (memory controller tuning, bank partitioning, NUMA configuration) and software optimizations (data layout restructuring, prefetching strategies, memory-aware scheduling). Through this comprehensive treatment of the memory-centric analysis pipeline—from trace collection through architectural modeling to co-design application—we provide researchers and practitioners with practical techniques for addressing memory bottlenecks in contemporary computing systems.

Gajaria, Dhruv Mayur

Trace levels of PtRu on NiMo foam electrodes towards hydrogen evolution reaction

Electrochemical water splitting plays a critical role in high purity hydrogen production. To lower capital cost and energy consumption, efficient catalysts are required to boost the hydrogen evolution reaction (HER), especially in alkaline media. Although PtRu alloy materials are still considered the state-of-the-art catalyst for the HER under alkaline media, large-scale application is hindered by its scarcity and high cost. NiMo alloy catalysts can be potential Pt-free alternatives to drive the sluggish kinetics of the HER under alkaline media, but their HER activity is still not ideal due to the limitation of Volmer step. Herein, we investigated the impact of trace levels of PtRu catalysts on NiMo electrodes towards the HER by incorporating advantages of both PtRu and NiMo catalysts to minimize cost and maintain a promising HER activity. Trace levels of PtRu catalysts from 0.0173 to 0.2648 mg cm −2 were loaded on commercial NiMo foam electrodes by a facile electrodeposition technique utilizing ppm concentration levels of PtRu in electrolyte. The results show that 0.0173 mg cm −2 PtRu loading on NiMo electrode can significantly enhance HER activity compared to the pristine NiMo foam electrode (Tafel slopes drop from ∼170 to ∼60 mV dec −1 ) due to the remarkable decline of energy barriers towards water dissociation and hydrogen adsorption. Meanwhile, the rate determining step (RDS) switches from the Volmer step to the Heyrovsky step when the PtRu loading increases to 0.0675 mg cm −2 . Promising catalytic stability is observed at 100 mA cm −2 over the course of 50 h with a PtRu loading of 0.1198 mg cm −2 . In conclusion, this work demonstrates a potential strategy to decrease the cost and simultaneously maintain superior HER performance by integrating trace levels of PtRu catalyst with NiMo foam electrodes.

Electrochemical water splitting

Irreversible Trace Metal Binding to Goethite Controlled by the Ion Size

The dynamics of trace metals at mineral surfaces influence their fate and bioaccessibility in the environment. Trace metals on iron (oxyhydr)oxide surfaces display adsorption–desorption hysteresis, suggesting entrapment after aging. However, desorption experiments may perturb the coordination environment of adsorbed metals, the distribution of labile Fe(III), and mineral aggregation properties, influencing the interpretation of labile metal fractions. In this study, we investigated irreversible binding of nickel, zinc, and cadmium to goethite after aging times of 2–120 days using isotope exchange. Dissolved and adsorbed metal pools exchange rapidly, with half times <90 min, but all metals display a solid-associated fraction inaccessible to isotope exchange. The size of this nonlabile pool is the largest for nickel, with the smallest ionic radius, and the smallest for cadmium, with the largest ionic radius. Spectroscopy and extractions suggest that the irreversibly bound metals are incorporated in the goethite structure. Rapid exchange of labile solid-associated metals with solution demonstrates that adsorbed metals can sustain the dissolved pool in response to biological uptake or fluid flow. Trace metal fractions that irreversibly bind following adsorption provide a contaminant sequestration pathway, limit the availability of micronutrients, and record metal isotope signatures of environmental processes.

58 GEOSCIENCES

Short-Term Inhibition and Long-Term Enhancement of Irreversible Trace Metal Binding to Goethite in Multi-Metal Systems

Iron (oxyhydr)oxide minerals are important sorbents of trace metals in aquatic environments. Adsorption–desorption hysteresis has been documented for trace metals after aging, suggesting that they become incorporated over time. We previously found that ion size controls the extent of irreversible metal binding of single metals to goethite. In this study, we evaluate how the presence of multiple metals influences irreversible binding. Mixed Ni–Zn and Ni–Cd solutions were aged with goethite at pH 7 for 2 days, 30 days, and 60 days, after which isotope exchange experiments were performed to assess the lability of the adsorbed metal pools. After 2 days of aging, Ni and Cd in mixed-metal systems were more labile than in single-metal systems, indicating that competitive adsorption may partially block irreversible binding on short time scales. After 60 days, all three metals had larger irreversibly bound fractions than in single-metal systems. X-ray absorption near-edge structure (XANES) spectroscopy indicates that irreversibly bound fractions correlate with incorporation into goethite. This study demonstrates that pools of coadsorbed metals are bioaccessible on a time scale of minutes. Cooperative effects promote the structural sequestration of even large trace metals, causing reactive transport models to likely overpredict metal mobility. Long-term metal entrapment processes hinder micronutrient availability, impact contaminant sequestration and critical mineral recovery, and yield complex pathways through which metal solubilization may be enhanced or hindered during redox cycling.

58 GEOSCIENCES

Trace benzene capture by decoration of structural defects in metal–organic framework materials

Abstract Capture of trace benzene is an important and challenging task. Metal–organic framework materials are promising sorbents for a variety of gases, but their limited capacity towards benzene at low concentration remains unresolved. Here we report the adsorption of trace benzene by decorating a structural defect in MIL-125-defect with single-atom metal centres to afford MIL-125-X (X = Mn, Fe, Co, Ni, Cu, Zn; MIL-125, Ti 8 O 8 (OH) 4 (BDC) 6 where H 2 BDC is 1,4-benzenedicarboxylic acid). At 298 K, MIL-125-Zn exhibits a benzene uptake of 7.63 mmol g −1 at 1.2 mbar and 5.33 mmol g −1 at 0.12 mbar, and breakthrough experiments confirm the removal of trace benzene (from 5 to <0.5 ppm) from air (up to 111,000 min g −1 of metal–organic framework), even after exposure to moisture. The binding of benzene to the defect and open Zn(II) sites at low pressure has been visualized by diffraction, scattering and spectroscopy. This work highlights the importance of fine-tuning pore chemistry for designing adsorbents for the removal of air pollutants.

Chemistry

Unraveling trace anomaly of supradense matter via neutron star compactness scaling

The trace anomaly Δ ≡ 1/3 −𝑃/𝜖 =1/3 −𝜙 quantifies the possibly broken conformal symmetry in supradense matter under pressure 𝑃 at energy density 𝜖. Perturbative QCD (pQCD) predicts a vanishing Δ at extremely high energy or baryon densities when the conformal symmetry is realized but its behavior at intermediate densities reachable in neutron stars (NSs) is still very uncertain. The extraction of Δ from NS observations strongly depends on the employed model for nuclear equation of state (EOS). Using the IPAD-TOV method based on an intrinsic and perturbative analysis of the dimensionless (IPAD) Tolman-Oppenheimer-Volkoff (TOV) equations that are further verified numerically by using 10 5 EOSs generated randomly with a metamodel in a very broad EOS parameter space constrained by terrestrial nuclear experiments and astrophysical observations, here we first show that the compactness 𝜉 ≡ 𝐺⁡𝑀 NS /𝑅⁢𝑐 2 ≡ 𝑀 NS /𝑅 of a NS with mass 𝑀 NS and radius 𝑅 scales very accurately with $\bar{Π}$ c ≡ $Π$ c · (1 +18⁢X/25) ≡ X/(1 +3⁢X 2 +4⁢X) · (1 +18⁢X/25) where X ≡ 𝜙 c = 𝑃 c /𝜖 c is the ratio of pressure over energy density at NS centers. The scaling of NS compactness thus enables one to readily read off the central trace anomaly Δ c = 1/3 −X directly from the observational data of either the mass-radius or red-shift measurements. Finally, we then demonstrate indeed that the available NS data themselves from recent X-ray and gravitational wave observations can determine model insensitively the trace anomaly as a function of energy density in NS cores, providing a stringent test of existing NS models and a clear guidance in a new direction for further understanding the nature and EOS of supradense matter.

nuclear astrophysics

Entanglement, trace anomaly, and confinement in QCD

We formulate confinement in quantum chromodynamics (QCD) as an entropic surface phenomenon. Quark and gluon quantum information is localized on a transverse, entangling two-sphere of radius 𝑅 𝐸⁢𝐸 ; at this radius the QCD vacuum—partitioned by a hadron into interior and exterior regions—reaches its maximal entanglement entropy. Lattice-QCD determinations of the scalar (trace) gravitational form factors fix both 𝑅 𝐸⁢𝐸 and the transverse trace-anomaly density 𝜌 ℎ ⁡(𝑅 𝐸⁢𝐸 ), yielding a parameter-free slope 𝑐 ℎ = 8⁢𝜋 2 ⁢𝑅𝑆$^2_{𝐸⁢𝐸}$𝜌 ℎ ⁡(𝑅 𝐸⁢𝐸 ) and a mechanical entropy 𝑆 𝐸⁢𝐸 ⁡(𝑦) = 𝑐 ℎ ⁢𝑦 that grows linearly with rapidity 𝑦. The entropy gradient ∂ 𝑅 𝑆 𝐸⁢𝐸 changes sign at 𝑅 𝐸⁢𝐸 : it pushes colored degrees of freedom outward for 𝑟 <𝑅 𝐸⁢𝐸 and pulls them inward for 𝑟 >𝑅 𝐸⁢𝐸 , thereby localizing them on the codimension-2 entangling two-sphere Σ ⊥ = 𝑆$^2_{𝑅_{𝐸⁢𝐸}}$ (which, in the infinite-momentum frame (IMF), projects onto the transverse plane)—the “information wall.” This provides a high-energy (large-𝑦) entropic confinement diagnostic that complements—rather than replaces—Wilson’s area-law criterion, which probes long-distance dynamics near the rest frame (𝑦 → 0). Imposing unitarity on an entropic ansatz for the amplitude yields 𝜎⁡(𝑠) ∝ 𝑦 𝛿 . World data favor 𝛿 = 2 for elastic 𝑝⁡𝑝⁡($𝑝\bar{⁡𝑝}$) scattering and heavy-quark photoproduction, whereas 𝜙 photoproduction favors a softer 𝛿 = 0.387. All extracted cross sections remain well below the Froissart-Martin bound. These results provide a confinement criterion quantified directly from nonperturbative QCD inputs, unifying the trace anomaly, entanglement entropy, and high-energy scattering within a single quantitative framework.

Color confinement

Trace Element Analyses of Micron-Size Particles and Statistical Determination of Minimum Detection Limits

Savannah River National Laboratory (SRNL) has developed expertise in producing homogeneous, ca. 1 m-diameter spherical particles of mixed-element components, wherein dopants can be varied from a trace constituent (ppm) to wt.% concentrations. The samples used for this work are nickel-doped cerium oxide microspheres produced by SRNL. They were initially selected as analogs for plutonium-doped uranium oxide particles and analyzed as part of a larger study to evaluate whether electron probe microanalyzers (EPMA) can be used to characterize nuclear materials as an alternative or complementary method to mass spectrometers. The five samples used in this study contained nominal compositions of 0, 0.004, 0.04, 0.4 and 4 wt.% Ni. They were analyzed by both an Agilent 7900 Q-ICP-MS at SRNL and the JEOL JXA&#x2;8530F Plus EPMA at the University of Minnesota. In addition to EPMA results (calibrated with high-precision Q-ICP-MS analyses) suggesting that the EPMA could address outstanding nuclear material characterization needs, these samples 1) showcase the ability of the EPMA to quantify not just trace concentrations, but trace concentrations in microparticles (1 m diameter, Fig. 1), and 2) offer a unique opportunity to evaluate the methodology for assessing the minimum detection limits of EPMA analyses.

McSwiggen, Peter [JEOL USA, 11 Dearborn Road, Peab